Re: [AMBER] TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff from Ross Walker on 2013-07-08 (Amber Archive Jul 2013)

From: Ross Walker <ross.rosswalker.co.uk>
Date: Mon, 08 Jul 2013 23:21:15 -0700

Hi Jeon,

The error is the NaNQ values for VDWAALS and EEL. This suggests you have
problems with your starting structure. Likely you have two atoms sitting
on top of each other. You can use the checkoverlap command in ptraj /
cpptraj or alternatively you can open it in a visualization program such
as VMD and take a look at the structure. You'll need to fix any steric
clashes before you can run a simulation.

All the best
Ross

On 7/8/13 11:12 PM, "전선희" <jeonsunny.naver.com> wrote:

>
>Hello.
>
>When I used AMBER10 with input file below,I met error message...
>
>TESTING RELATIVE ERRORover r ranging from 0.0 to cutoff.
>
>How can I pass the this error message?????
>
>I need your help~~
>
>-------------------------------------------------------
>
> Amber 10 SANDER 2008
>
> -------------------------------------------------------
>
>
>
>Run on 07/08/2013 at 17:38:27
>
> [-O]verwriting output
>
>
>
>FileAssignments:
>
> MDIN: min1.in
>
>
>MDOUT: min1.out
>
>
>INPCRD:11mersol.inpcrd
>
>
> PARM: 11mersol.prmtop
>
>
>RESTRT:min1.restrt
>
>
> REFC: 11mersol.inpcrd
>
>
>MDVEL: mdvel
>
>
> MDEN: mden
>
>
>MDCRD: mdcrd
>
>
>MDINFO:mdinfo
>
>
>INPDIP:inpdip
>
>
>RSTDIP:rstdip
>
>
>
>
>
>
> Here is the input file:
>
>
>
>11merminimization
>
>
> &cntrl
>
>
> imin = 1,
>
>
> maxcyc = 2000,
>
>
> ncyc = 1000,
>
>
> ntb = 1,
>
>
> ntr = 1,
>
>
> cut = 10
>
>
>/
>
>
>Holdthe DNA fixed
>
>
>500.0
>
>
>RES1 22
>
>
>END
>
>
>END
>
>
>
>
>
>
>
>--------------------------------------------------------------------------
>------
>
> 1. RESOURCE USE:
>
>--------------------------------------------------------------------------
>------
>
>
>
>Flags:
>
>
> getting new box info from bottom of inpcrd
>
> INFO: Old style inpcrd file read
>
>
>
>peek_ewald_inpcrd: Box info found
>
>Largestsphere to fit in unit cell has radius = 30.160
>
>New format PARM file being parsed.
>
>Version = 1.000 Date = 01/22/13 Time =15:24:05
>
> NATOM = 20250 NTYPES = 18 NBONH = 19786 MBONA = 496
>
> NTHETH = 588 MTHETA = 762 NPHIH = 1260 MPHIA = 1344
>
> NHPARM = 0 NPARM = 0 NNB = 29924 NRES = 6554
>
> NBONA = 496 NTHETA = 762 NPHIA = 1344 NUMBND = 39
>
> NUMANG = 76 NPTRA = 42 NATYP = 28 NPHB = 1
>
> IFBOX = 1 NMXRS = 33 IFCAP = 0 NEXTRA = 0
>
> NCOPY = 0
>
>
>
>
>
> Memory Use Allocated
>
> Real 1380212
>
> Hollerith 128056
>
> Integer 510434
>
> Max Pairs 11664000
>
> nblistReal 243000
>
> nblist Int 807800
>
> Total 63893 kbytes
>
>Duplicated 0 dihedrals
>
>Duplicated 0 dihedrals
>
>
>
> BOX TYPE: RECTILINEAR
>
>
>
>--------------------------------------------------------------------------
>------
>
> 2. CONTROL DATA FOR THE RUN
>
>--------------------------------------------------------------------------
>------
>
>
>
>
>
>
>
>
>Generalflags:
>
> imin = 1, nmropt = 0
>
>
>
>Natureand format of input:
>
> ntx = 1, irest = 0, ntrx = 1
>
>
>
>Natureand format of output:
>
> ntxo = 1, ntpr = 50, ntrx = 1, ntwr =
>500
>
> iwrap = 0, ntwx = 0, ntwv = 0, ntwe =
> 0
>
> ioutfm = 0, ntwprt = 0, idecomp = 0,rbornstat=
> 0
>
>
>
>Potentialfunction:
>
> ntf = 1, ntb = 1, igb = 0, nsnb =
>25
>
> ipol = 0, gbsa = 0, iesp = 0
>
> dielc = 1.00000, cut = 10.00000, intdiel = 1.00000
>
> scnb = 2.00000, scee = 1.20000
>
>
>
>Frozenor restrained atoms:
>
> ibelly = 0, ntr = 1
>
>
>
>Energyminimization:
>
> maxcyc = 2000, ncyc = 1000, ntmin = 1
>
> dx0 = 0.01000, drms = 0.00010
>
>
>
>Ewaldparameters:
>
> verbose = 0, ew_type = 0,nbflag = 1, use_pme =
> 1
>
> vdwmeth = 1, eedmeth = 1, netfrc = 0
>
> Box X = 60.320 Box Y = 68.060 Box Z = 61.996
>
> Alpha = 90.000 Beta = 90.000 Gamma = 90.000
>
> NFFT1 = 60 NFFT2 = 72 NFFT3 = 64
>
> Cutoff= 10.000 Tol =0.100E-04
>
> Ewald Coefficient = 0.27511
>
> Interpolation order = 4
>
>
>
> LOADING THE CONSTRAINED ATOMS AS GROUPS
>
>
>
>
>
> 5. REFERENCE ATOM COORDINATES
>
>
>
>
>
> ----- READING GROUP 1; TITLE:
>
> Hold the DNA fixed
>
>
>
>
> GROUP 1 HAS HARMONIC CONSTRAINTS 500.00000
>
> GRP 1RES 1 TO 22
>
> Number of atoms in this group = 694
>
> ----- END OF GROUP READ -----
>
>
>
>--------------------------------------------------------------------------
>------
>
> 3. ATOMIC COORDINATES AND VELOCITIES
>
>--------------------------------------------------------------------------
>------
>
>
>
> begin time read from input coords = 0.000 ps
>
>
>
> Number of triangulated 3-point watersfound: 6512
>
>
>
> Sum of charges from parm topology file= 0.00000013
>
> Forcing neutrality...
>
>
>
>--------------------------------------------------------------------------
>------
>
> 4. RESULTS
>
>--------------------------------------------------------------------------
>------
>
>
>
> ---------------------------------------------------
>
> APPROXIMATING switch and d/dx switch usingCUBIC SPLINE INTERPOLATION
>
> using 5000.0 points per unit in tabled values
>
> TESTINGRELATIVE ERROR over r ranging from 0.0 to cutoff
>
>CHECK switch(x): max rel err = 0.3338E-14 at 2.509300
>
>CHECK d/dx switch(x): max rel err = 0.8155E-11 at 2.730040
>
> ---------------------------------------------------
>
>Local SIZE OF NONBOND LIST = 5997049
>
>TOTAL SIZE OF NONBOND LIST = 5997049
>
>
>
>
>
> NSTEP ENERGY RMS GMAX NAME NUMBER
>
> 1 NaNQ NaNQ 2.5067E+06 C2' 690
>
>
>
> BOND = 547139.9071 ANGLE = 2188.4961 DIHED = 504.1794
>
> VDWAALS = NaNQ EEL = NaNQ HBOND =
>0.0000
>
> 1-4 VDW = 680.4379 1-4 EEL = -2982.8481 RESTRAINT =
>0.0000
>
>
>
>jeonsunny님의 블로그
>안녕하세요.
>
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Received on Mon Jul 08 2013 - 23:30:03 PDT